Hi Carlos, The pgSnp track type is very new and has not yet been added to all the documentation (adding it to the documentation is on our "To do" list). You can still follow the general directions to creating tracks in the browser (see following resources) with some supplemental information I've included in this email:
src/product/README.trackDb http://genomewiki.ucsc.edu/index.php/Local_tracks_at_mirror_sites src/hg/makeDb/trackDb/README (<-- how trackDb entries function - general information) Here is the supplemental information you'll need for the pgSnp format: In the trackDb documentation, you won't see pgSnp listed as a track type, but it is a valid type. For the type line of your trackDb entry you will use: type pgSnp. Here is an example trackDb entry I created to make sure everything worked: track katrinaPgSnp shortLabel My SNPs longLabel My SNP Track of Example SNPs visibility full type pgSnp group varRep In my example above, in order to display, I'll need to have a table called katrinaPgSnp, my track will be part of the Variation and Repeats group, and it will be set to full by default. Most of the information in http://genome.cse.ucsc.edu/FAQ/FAQformat.html#format10 is applicable to the pgSnp format in general (not just to custom tracks). Things like the fields and options are the same for local tracks. The documentation about creating local tracks suggests that most track types have a special loader program, but for pgSnp you'll need to use the hgLoadBed program. To load a pgSnp table, you need to run hgLoadBed with a file containing your data (in the example below we called it myPgSnpFile.txt, which should be tab delimited, no headers) and with the -sqlTable argument plus the appropriate .sql file (in this case you'll use pgSnp.sql). Here is an example adapted from one of our pg tracks: hgLoadBed $database $track myPgSnpFile.txt -sqlTable=$HOME/kent/src/hg/lib/pgSnp.sql -renameSqlTable -tab When -sqlTable is used, it's up to that .sql file to define the indexes that will be built. hg/lib/pgSnp.sql includes the INDEX (chrom,bin). To see the complete usage statement for hgLoadBed (with more information about each argument), simply type it at the command line with no arguments. I believe this is all the supplemental information you'll need, but please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Carlos Javier Borroto wrote, On 4/25/2011 3:04 PM: > Hi Katrina, > > Right now I'm using BED detail with itemRgb as I was able to find > searching in the mailing list and you kindly point me to, but in order > to use this I had to come up with a script to put the right r,g,b > color code depending on the function my SNP software is calling, or if > the software gives a rsID I just grab the function from snp132 track. > But this was cumbersome and I'm not getting present and future extras > from "Personal Genome SNP format". So even if there is not an option > to change the color scheme, I would like to host my SNPs track in this > format. > > I tried to look for pgSnp type in: > src/hg/makeDb/trackDb/README > > There is not such a thing and I couldn't find any other type I could > think is the correct one to put in my "trackDb.ra" file. This website > you comment and I already checked: > http://genome.cse.ucsc.edu/FAQ/FAQformat.html#format10 > > Only talks about custom tracks not local tracks which is what I would > like to use, I also couldn't find the right utility to load the table > into the database(like hgLoadBed). If you could point me to a > documentation to use pgSnp type track as a local track I would highly > appreciated it. > > Thank you very much for your help. > PS: Should I ask this type of question at [email protected]? > PPS: Would it be better to adjust the reply-to of the list to the list > address, I keep forgetting to use reply-all. > -- > Carlos Borroto > Baltimore, MD > > > > On Mon, Apr 25, 2011 at 5:21 PM, Katrina Learned <[email protected]> wrote: > >> Hi Carlos, >> >> For directions on loading your own track into your mirror see: >> http://genomewiki.ucsc.edu/index.php/Adding_New_Tracks_to_a_browser_installation >> Additionally, the "See Also" section of that page, which provides more >> helpful resources: "For a generic discussion of how to load any type of >> track into your local browser mirror, refer to the document in the source >> tree src/product/README.trackDb and the discussion of how the trackDb >> entries function in src/hg/makeDb/trackDb/README". >> >> The Personal Genome SNP would probably work best for your purposes, however >> the colors displayed cannot be based on a SNP's function. In order to color >> the track in this way, you would have to use a BED detail format, which >> wouldn't automatically calculate all that the Personal Genome SNP format >> does. For more information about these track types, see this previously >> answered Mailing List question: >> https://lists.soe.ucsc.edu/pipermail/genome/2011-February/025155.html >> >> Please contact the mail list ([email protected]) again if you have any >> further questions. >> >> Katrina Learned >> UCSC Genome Bioinformatics Group >> Carlos Javier Borroto wrote, On 04/22/11 13:50: >> >>> Hi, >>> >>> Is it possible to create a "Personal Genome SNP" local track(not just >>> a custom) in a local mirror? What track type can I use? >>> >>> Also, I see the "Personal Genome SNP" custom track detail page gives >>> information about the function of the SNP, but can this information be >>> shown using a color code like in snp132 instead of the allele >>> frequency coloring? >>> >>> Thanks, >>> -- >>> Carlos Borroto >>> Baltimore, MD >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >>> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
